It is a rock formation that appears to be a gigantic tree. The Tree of Beginning is actually a living organism made up of crystal that feeds on sunlight. It has a symbiotic connection with a Mew that lives within it, and it is home to many kinds of ancient Pokémon thought to be extinct. It has a "circulatory system" of sorts that distributes nutrients to the crystals throughout its body. It also has a complex antibody system that takes the form of Fossil Pokémon that attack humans and machines within it, as well as guardians in the form of the Legendary titans.

The crystals of the tree actually seem to extend far beyond the formation itself, emerging from the ground like roots throughout the surrounding areas. The Tree of Beginning is located in a mountain range north of Pewter City and Mt. Moon, slightly outside of the borders of the Kanto region.

Many years ago, Sir Aaron sacrificed himself to transfer his power to Mew so that Mew could restore peace to the land and save it from two raging Pokémon armies battling each other. In the present, in the eighth movie, Mew, when attacked by Kidd's two Weavile (whose job was only to put a tracking device on it), teleported to the Tree of Beginning with Pikachu and Meowth due to injuries Pikachu received in the battle. Ash, Brock, May, Max, and Lucario set out to find Pikachu, since Mew had a history of taking toys from the attic and never returning them. Inside the Tree of Beginning, they were attacked by Regirock, Regice, and Registeel. Lucario fought them off but none of his attacks worked on the white blood cells, which ate Jessie, James, Brock, May, Max, Kidd, and Ash. They wouldn't swallow Lucario, however, not perceiving Pokémon as a "threat".

Mew brought them all back to life, though unfortunately this put the immune system into shock and dooming the tree to die unless the same aura procedure with Mew was performed. Ash and Lucario transferred their power to Mew in order to restore the tree to full health, Lucario finishing the process, sacrificing himself as Sir Aaron had done many years ago. The tree was restored to full health and the Legendary titans stopped attacking the humans.